Biology subjects

Makar, A.

Publications and source records attributed to Makar, A..

4 recordsLinked to original sources

bioRxiv2026

The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells

Mass spectrometry-based single cell proteomics (SCP) is rapidly emerging as a powerful approach for biological research, with applications extending beyond in-vitro cancer cell lines. Recent advances make it possible to apply SCP to ex-vivo human cells from tissues such as the brain and pancreas, as well as to technically challenging immune populations such as neutrophils. However, these analyses remain more challenging and typically result in reduced proteomic coverage. To support the development of robust workflows for SCP data acquisition and analysis, we systematically evaluated multiple DIA search engines, search engine settings, the inclusion of high-load library samples in single-cell search spaces, the impact of contaminants, and the quantitative properties of identified proteins. These comparisons were performed across two major instrumentation platforms, Orbitrap Astral and timsTOF SCP, and across A549, RKO cells and neutrophils, three cell types differing in size and protein content. Our work here provides guidelines on the software parameters to use for SCP, instrument specific results and cell dependent optimizations of high-load libraries, as well as novel evaluation of the quantitative properties of proteins for single cell and low input proteomics.

biochemistry↗

bioRxiv2025

The "Grove-First" Framework: Starting in the Grove to Find Therapies for Huanglongbing

Citrus greening disease, also known as huanglongbing (HLB), is the most serious vector-borne bacterial disease of citrus world-wide1,2. There is an immediate global need to provide the citrus industry with relief from HLB and a return to profitable citrus production. Standard screening methods for HLB therapeutic treatments typically involve various laboratory-based assays to select treatments with antimicrobial properties3, which then advance to greenhouse and eventually field testing in a workflow that takes multiple years. Unlike traditional lab-first screening, we present a design of experiments framework4,5, referred to as Grove-First, that rapidly screens treatments with regulatory-friendly profiles in commercial citrus groves using trunk injection to select treatments that improve tree health and fruit yield over the course of a single growing season. Using this framework, we identified candidate treatments with effects comparable to or better than the standard oxytetracycline (OTC) on visual tree-health and/or yield indices in an initial screen of HLB-positive 8-year-old Valencia sweet orange trees. Expanded trials in commercial citrus groves allowed us to validate the initial screening results at other locations and in other citrus varieties. Grove-First rapidly accelerated the identification and large-scale field testing of HLB therapies, some of which are available for growers to use immediately and others that require further field testing and/or regulatory actions.

plant biology↗

bioRxiv2022

Croatian Genetic Heritage: Renewed Y Chromosome Story a Decade Later

AimTo analyze an additional set of Y-Chromosome genetic markers to acquire a more detailed insight into the diversity of the Croatian population. MethodsThe total number of 518 Yfiler Plus profiles were genotyped. Allele, haplotype frequencies, and haplotype diversity were calculated using the STRAF software package v2.0.4. Genetic distances were quantified by Rst using AMOVA online tool from the YHRD. The evolutionary history was inferred using the neighbor-joining method of phylogenetic tree construction in MEGAX software. Whit Atheys Haplogroup Predictor v5 was used for additional comparison with available regional and other European populations. ResultsThe total of 507 haplotypes were used for genetic STR analysis. The interpopulation study on 17 Y-STR markers shows the lowest genetic diversity between the Croatian and Bosnian-Herzegovinian populations and the highest between the Croatian and Irish populations. Additional interpopulation comparison with the original 27 Y-STR markers (for the population with available data) was also performed. A total of 518 haplotypes were used in the determination of haplogroup diversity. Haplogroup I with its sublineage I2a expressed the highest prevalence. Haplogroup R, with its major sublineage R1a, is the second most abundant in the studied Croatian population, except for the subpopulation of Hvar, where E1b1b is the second most abundant haplogroup. Rare haplogroups also confirmed in this study are L, T, and Q. G1 is detected for the very first time in the Croatian population. ConclusionNew insight into differences between examined subpopulations of Croatia and their possible (dis)similarities with neighboring abroad populations was notified.

evolutionary biology↗

bioRxiv2019

Is asthma associated with exposure to smoke from a coal mine fire?

In 2014, a fire at the Hazelwood open cut coal mine (Victoria, Australia) burned for about 6 weeks. Residents of the adjacent town of Morwell were exposed to high levels of fine particulate matter (PM2.5) during this period. Three and a half years after the event, this study aimed to investigate the long-term impact of short-term exposure to coal mine fire smoke on asthma.\n\nA cross-sectional analysis was undertaken on a group of exposed participants with asthma from Morwell (n=165) and a group of unexposed participants with asthma from the control town of Sale (n=64). Town exposure status was determined by modelled PM2.5 data for the mine fire period. Respiratory symptoms were assessed with a validated respiratory health questionnaire and symptom severity score. Asthma control was assessed with an asthma control questionnaire. Lung function testing included spirometry, bronchodilator response, and fraction of exhaled nitric oxide.\n\nThere was no evidence that exposed Morwell participants had more severe asthma symptoms, worse lung function, or more eosinophilic airway inflammation compared to unexposed Sale participants. However there was some evidence that Morwell participants had more uncontrolled than well-controlled asthma, compared to the participants from Sale (adjusted relative risk ratio 2.71 95%CI: 1.02, 7.21, p=0.046).\n\nThree and a half years after exposure, coal mine fire smoke does not appear to be associated with more severe asthma symptoms or worse lung function, but may be associated with poorer asthma control.\n\nSummary take home messageIn people with asthma, short-term coal mine fire smoke exposure does not appear to have long-term impact on severity of asthma symptoms, lung function or eosinophilic airway inflammation, but may affect asthma control.

epidemiology↗